Contacts of the helix formed by residues 255 - 266 (chain O) in PDB entry 3K9Q
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 255 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253O ASP 4.0 9.0 - - - +
254O VAL* 1.3 79.5 - - - +
256O VAL* 1.3 65.6 + - - +
257O GLU* 3.5 18.0 + - - +
258O GLN* 3.0 43.6 + - - +
259O VAL* 3.1 16.3 + - - +
299O VAL* 4.0 8.1 - - - -
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Residues in contact with VAL 256 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255O THR* 1.3 73.7 - - - +
257O GLU* 1.3 79.1 + - - +
259O VAL* 3.2 2.6 + - - +
260O ASN* 2.9 41.9 + - - +
294O ALA 5.2 1.3 - - - +
297O THR* 3.9 33.4 - - + +
298O ARG* 4.2 2.5 - - - -
299O VAL* 3.8 27.6 - - + +
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Residues in contact with GLU 257 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255O THR* 3.1 20.8 + - - +
256O VAL* 1.3 93.1 + - + +
258O GLN* 1.3 57.1 + - + +
260O ASN* 3.9 5.0 - - - +
261O GLU* 2.9 36.3 + - + +
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Residues in contact with GLN 258 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167O PHE* 3.8 17.6 - - + -
251O LYS* 5.9 2.8 - - - +
253O ASP 3.8 5.4 + - - +
254O VAL* 3.3 14.6 - - - +
255O THR* 3.0 38.3 + - - +
257O GLU* 1.3 74.0 - - + +
259O VAL* 1.3 66.8 + - - +
261O GLU* 3.9 4.9 - - - +
262O ALA* 3.0 26.2 + - - +
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Residues in contact with VAL 259 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163O LEU* 4.5 11.2 - - + -
167O PHE* 4.0 15.5 - - + -
249O LEU* 5.3 0.4 - - + -
254O VAL* 3.6 22.0 - - + -
255O THR 3.1 13.2 + - - +
256O VAL* 3.6 6.7 - - - +
258O GLN* 1.3 78.6 - - - +
260O ASN* 1.3 63.5 + - - +
262O ALA* 3.2 2.3 + - - +
263O MET* 3.1 26.3 + - + +
292O PHE* 4.4 6.3 - - + -
297O THR* 4.0 10.5 - - + -
299O VAL* 5.1 0.7 - - + -
308O VAL* 4.0 16.8 - - + -
310O VAL* 3.6 30.3 - - + -
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Residues in contact with ASN 260 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256O VAL* 2.9 38.4 + - - +
257O GLU* 3.9 5.5 - - - +
259O VAL* 1.3 74.6 - - - +
261O GLU* 1.3 61.6 + - - +
263O MET* 3.1 3.3 + - - +
264O LYS* 3.0 19.2 + - - +
273O TYR* 3.4 24.1 - - - +
292O PHE* 3.3 16.5 - - - -
294O ALA* 3.4 28.0 + - + +
297O THR* 2.7 23.7 + - - -
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Residues in contact with GLU 261 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257O GLU* 2.9 21.2 + - + +
258O GLN* 3.9 5.8 - - - +
260O ASN* 1.3 76.9 - - + +
262O ALA* 1.3 62.3 + - - +
264O LYS* 3.3 21.3 + - + +
265O ASN* 3.0 44.6 + - - +
273O TYR* 5.4 0.4 - - - -
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Residues in contact with ALA 262 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162O VAL* 3.8 20.4 - - + +
166O ASP* 3.2 26.6 - - - +
167O PHE* 4.1 11.0 - - + -
258O GLN 3.0 20.2 + - - +
259O VAL 3.6 4.0 - - - +
261O GLU* 1.3 75.5 - - - +
263O MET* 1.3 61.6 + - - +
265O ASN* 3.5 9.6 + - - +
266O ALA* 3.3 18.2 + - - +
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Residues in contact with MET 263 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159O VAL* 3.4 35.0 - - + +
162O VAL* 3.7 23.8 - - + -
163O LEU* 3.7 25.1 - - + -
167O PHE* 5.9 0.2 - - + -
259O VAL* 3.1 19.0 + - + +
260O ASN 3.1 6.0 + - - +
262O ALA* 1.3 72.5 - - - +
264O LYS* 1.3 63.6 + - - +
266O ALA* 3.1 11.5 + - - +
267O SER* 3.4 9.9 + - - -
271O PHE* 3.7 31.5 - - + -
272O GLY 5.8 0.2 - - - +
273O TYR* 4.3 3.2 - - + +
292O PHE* 3.4 45.3 - - + -
310O VAL* 4.9 0.4 - - + -
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Residues in contact with LYS 264 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260O ASN 3.0 12.5 + - - +
261O GLU* 3.6 23.8 + - + +
263O MET* 1.3 75.8 - - - +
265O ASN* 1.3 65.8 + - - +
267O SER* 3.0 25.0 + - - +
273O TYR* 3.7 47.2 - - + +
275O GLU* 5.6 1.3 - - - +
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Residues in contact with ASN 265 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261O GLU* 3.0 37.9 + - - +
262O ALA* 3.8 8.9 - - - +
263O MET 3.3 0.2 - - - -
264O LYS* 1.3 80.6 - - - +
266O ALA* 1.3 59.3 + - - +
267O SER 3.3 3.0 + - - +
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Residues in contact with ALA 266 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162O VAL* 3.4 32.8 - - + -
262O ALA 3.3 5.9 + - - +
263O MET 3.1 10.7 + - - +
265O ASN* 1.3 73.9 - - - +
267O SER* 1.3 65.5 + - - +
268O ASN* 3.7 13.5 + - - -
271O PHE* 3.9 13.3 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il